Method and system for managing storage units are provided. A free space module scans a storage unit data structure and a reference data structure to generate an intermediate data structure that identifies storage units that are not referenced by any storage unit client. A lookup module is initiated and the storage unit clients are notified that all new references to any storage unit should be verified with the lookup module. The free space module then verifies if any of the storage units in the intermediate data structure have been referenced since the intermediate data structure was created. Any referenced storage units are removed from the intermediate data structure and a data structure identifying unreferenced storage units is generated. The data structure is then used to allocate the identified storage units.